Some fleets were sending messages via courier drones early in the campaign, I assume they were loaded from planets? Do they take transport space like fighters and pinnaces? Is remembering to carry them a massive pain and a good reason to use the ICN (at least in normal times)? 
Presumably small ships stationed at every warp point could act as a relay, either by sending messages directly or catching and forwarding drones?
From the shipyards section, if MSY is a mobile shipyard, what is MS?
I won't answer the courier drone questions, as I think those have already been answered very capably by others. In the early days of the campaign, all inter-system comms were by either courier drone or ship. The fastest method of comms would have been to station small ships with communications modules on both sides each warp point along a critical warp chain, which would result in near light-speed comms. that's pretty expensive, though, especially in reduced-growth, reduced construction speed campaign.
MSY's are indeed mobile shipyards and are smaller and somewhat less capable than regular SY's. MS are machine shops, and are capable of repairing and refitting ships, but not construction.
All of that means that the Alliance’s massive commitment of ships languishes in the Villiers system, waiting, while the Zir apparently dither
...
the Zir cannot come to grips with either the Alliance’s constant pushing to take action, or indeed, on what action to take
I think the correct phrase to use is "smeg, or get off the pot".
the Alliance Navy has decided to push forward with a massive program of refits to modernize the fleet
...
The Rehorish high command has gone on alert, and no new refits will be started
Someone on the D'Bringi side is going to notice this at some point.
Something is seriously wrong with the Alliance's communications, I'd say.
The Kingdom has mothballed a significant percentage of the fleet now that it is clear that the Alliance is no threat, and is focusing on expanding its territory and economy.
For their sake, I hope this information was kept off the Alliance ICN.
The Mintek have almost as many shipyards as the CU and Bjering have put together, despite having less income than either. I thought they preferred large hulls because they used Dreadnoughts early on. That said, they seem to have a bit of an advantage because they've upgraded their whole fighter force, whereas the other major powers are still in progress or not started.
I just noticed that as well. That is an artifact of my not paying attention to details. The Mintek have not come close utilizing all of their home system's shipyards at any point, and really should have mothballed a lot of them at some point, given the economic crunch they've been under at various times. In addition, they successfully seized the shipyards over both the Alowan and the Bedu home worlds, further bolstering their yard capacity.
As for the fighter advantage, the difference between an F1 and an F0 is not huge. The F1 can carry 50% more external ordnance, 3 weapons instead of 2 for the F0, but has the same loaded speed. The F1 does have twice the endurance of the F0, and better sensor range, though. Having a homogenous force of F1's will be an advantage but will not make up for being seriously outnumbered.
The Alliance intends to significantly boost its shipyard capacity, but it is currently locked into major round of refits. Both the Alliance and the Colonial Union believe that they have under-invested in shipyards and will seek to change that in the future, but there are many other commitments as well.
The Alliance seems by far the strongest side in terms of income and military, but they seem to be at risk of over-extension and paralysis, because of the number of races they are maintaining as associate members.
Assuming it isn't a spoiler, could you put the current tech level of the Aurarii, Chirq, Doraz, Lothar, Torqual and Zir, and also the Major Races?
Mintek Universal Union is HT-9, on its way to HT-10
Bjering Consolidate is HT-9, well on their way to HT-10
Colonial Union is HT-8, just starting out on R&D for HT-9
Alliance is HT-9, just starting out on R&D for HT-10
Alliance partners and treaty members:
Aurarii Republic is HT-9, working on developing HT-9 systems
Bir Meritocracy is HT-1. on its way towards HT-2 with assistance from the Alliance
Chirq Cooperative is HT-3, just starting out R&D in HT 4
Doraz Contingency is HT-7, well on its way to HT-8
Kingdom of Lothar is HT-10, on its way to HT-11 (Note, the Kingdom has gone to lengths to conceal its true tech level from the Alliance, and has successfully convinced them that they are at the same tech level)
Torqual Free State is HT-7, currently developing HT-7 systems
The Zir Contemplative Union is HT-7, on its way towards HT-8
The upshot is that the Mintek have a small tech lead over the Alliance, and a bigger tech lead over the Colonial Union, but is slightly behind the Bjering. Of the Alliance member races, the most militarily and economically important are the Zir, Torqual, and Doraz, and all of these are HT-7, which is pre-fighter. All three are advancing relatively quickly, though, as the Alliance is assisting their R&D efforts.
